Phase I: The R43 phase of this project aims to develop and demonstrate a capillary gel electrophoresis (CGE) based multidimensional protein separation platform capable of providing significant analyte concentration and extremely high resolving power for handling complex protein mixtures prior to mass spectrometry detection. In comparison with conventional SDS-PAGE-based proteome approaches, the proposed CGE/capillary reversed-phase liquid chromatography (CRPLC) proteome technology will be highly automated and offer robust and high throughput fractionation of whole proteins for top-down proteomics while avoiding analyte dilution and loss in an integrated platform. By coupling with a nanoscale trypsin membrane reactor, the ultrafast proteolytic digestion of proteins resolved and eluted from the CGE-based separations enables the combined top-down/bottom-up characterization of post-translational modifications in complex proteomes. Research efforts in the R43 phase will address early implementation, optimization, and demonstration of the proposed proteome technology using yeast cell lysates.